Recent improvements to the SMART domain-based sequence annotation resource

By Ivica Letunic, L. Goodstadt, Nicholas J. Dickens, Tobias Doerks, Jörg Schultz, Richard Mott, F. Ciccarelli, Richard R. Copley, Chris P. Ponting, Peer Bork. Nucleic Acids Res., 2002

689 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/877d2ae34a259ccc6781b8525ab169e771bf1878

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Citations in the corpus

Database resources of the National Center for Biotechnology Information: update (2004, positive): “The CDD contains over 11 000 position-speciﬁc score matrices representing domains taken from the Simple Modular Architecture Research Tool (SMART) (26), Pfam (27) and recently, from domain alignments derived from both COGs and KOGs.”
GlobPlot: exploring protein sequences for globularity and disorder (2003, methodology): “There are many methods, such as SMART (Simple Modular Architecture Research Tool) (3), PRODOM (4) , Pfam (5,6), PROSITE (7) and ELM (Eukaryotic Linear Motif, http:// elm.eu.org) (8), available for finding globular domains (e.g. SH3, TyrKc, active sites) and linear motifs (e.g. SH3 ligands, LXXLL nuc”
MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress (2007, methodology): “Distinctively, in case of Mγ proteins a larger MADS domain of 83 amino acids was detected, followed by a coiled coil region and a region of unknown complexity as indicated by Simple Modular Architecture Research Tool (SMART) version 3.4.”
InterProScan: protein domains identifier (2005, background): “ProDom (6) BlastProDom (Blastall) (4) PRINTS (7) FingerPrintScan (8) SMART ( 9 ) Hmmpfam (http://hmmer.wustl.edu/) TIGRFAMs (10) Hmmpfam (http://hmmer.wustl.edu/) Pfam (11) Hmmpfam (http://hmmer.wustl.edu/) PROSITE (12) ScanRegExp + ProfileScan (13) PIRSF (14) Hmmpfam (http://hmmer.wustl.edu/) SUPER”
Database resources of the National Center for Biotechnology (2003, background): “The CDD contains PSI-BLAST-derived Position Specific Score Matrices representing domains taken principally from two public protein domain collections, the Simple Modular Architecture Research Tool (SMART) (24), and Pfam (25), but also draws from domains defined by NCBI researchers.”
UniProt: the Universal Protein knowledgebase (2004, background): “InterPro is an integrated resource of protein families, domains and sites that amalgamates the efforts of the member databases: Pfam (11), PROSITE (12), PRINTS (13), ProDom (14), SMART (15), PIRSF (16), Superfamily (17) and TIGRFAMs (18).”
Molecular and Phylogenetic Analyses of the Complete MADS-Box Transcription Factor Family in Arabidopsis Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.011544. (2003, methodology): “SMART (Simple Motif Architecture Research Tool) version 3.4 (Schultz et al., 1998; Letunic et al., 2002) was used to annotate the motifs found by MEME.”
The properties of protein family space depend on experimental design (2005, methodology): “Examples of such databases are Pfam (Bateman et al., 2004), TIGRFAMS (Haft et al., 2003) and SMART (Letunic et al., 2002).”
PANTHER: a library of protein families and subfamilies indexed by function. (2003, methodology): “HMM libraries, such as PANTHER, Pfam, and SMART, are used primarily to recognize and annotate conserved motifs in protein sequences.”
The ankyrin repeat as molecular architecture for protein recognition (2004, methodology): “…repeat sequences in 1871 proteins identified from the Swissprot and SP-TrEMBL databases (Bateman et al. 2002), while the SMART database contains 19,276 ankyrin repeat sequences in 3608 proteins identified from the nonredundant protein database (NRDB; Schultz et al. 1998; Letunic et al. 2002).”
Distribution and evolution of von Willebrand/integrin A domains: widely dispersed domains with roles in cell adhesion and elsewhere. (2002, methodology): “As of 24 March 2002 the SMART nonredundant database (nrdb) (a merger of swissprot, swissnew, sptrembl, and sptremblnew) contained 948 proteins containing 1196 VWA domains, with new additions being deposited regularly (Letunic et al., 2002; http://smart. embl-heidelberg.de/).”
Pfam: clans, web tools and services (2005, background): “Inﬂuenced by SMART (12) and PROSITE (13), the graphical representation of domains has been updated on the website (Table 2).”
Short Communication Homology between the human cytomegalovirus RL11 gene family and human adenovirus E3 genes (2003, methodology): “…1998; Ewing et al., 1998), and analysed using the GCG suite (Accelrys), Ptrans for sequence translation (Taylor, 1986), SignalP 2.0 for predicting signal cleavage peptides (Nielsen et al., 1997) and the TMHMM2 module of the Smart suite for predicting transmembrane domains (Letunic et al., 2002).”
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 (2003, background): “This is an integrated resource of protein families, domains and sites which amalgamates the efforts of the member databases which are currently PROSITE (23), PRINTS (24), Pfam (25), ProDom (26), SMART (27) and TIGRFAMs (28).”
The Pfam protein families database (2011, background): “First, the SMART database of protein domains ( 8 ) and Pfam each contain many entries that are not available in the other, and in other cases the family memberships differ markedly.”
ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins (2003, methodology): “All matches inside globular domains identified with the SMART and Pfam domain databases (3,4) are subtracted.”